The following softwares have been installed in March 2022

• CONCOCT version: 1.1.0

  Description:A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.

  URL: https://concoct.readthedocs.io/en/latest/index.html
  

  Command to load its environment: module load bioinfo/concoct/1.1.0

• picrust2 version: 2.4.2

  Description: a software for predicting functional abundances based only on marker gene sequences.

  URL: https://github.com/picrust/picrust2
  

  Command to load its environment: module load bioinfo/picrust2/2.4.2

• mosdepth version: 0.3.3

  Description: Stats on coverage and depth (NGS)

  URL: https://github.com/brentp/mosdepth
  

  Command to load its environment: module load bioinfo/mosdepth/0.3.3

• ppanggolin version: 1.2.74

  Description: software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequence

  URL: https://github.com/labgem/PPanGGOLiN
  

  Command to load its environment: module load bioinfo/ppanggolin/1.2.74

• panacota version: 1.3.1

  Description: PANgenome with Annotations, COre identification, Tree and corresponding Alignments

  URL: https://github.com/gem-pasteur/PanACoTA
  

  Command to load its environment: module load bioinfo/panacota/1.3.1

• panaroo version: 1.2.10

  Description: An updated pipeline for pangenome investigation

  URL: https://github.com/gtonkinhill/panaroo
  

  Command to load its environment: module load bioinfo/panaroo/1.2.10

• flye version: 2.9

  Description: De novo assembler for single molecule sequencing reads using repeat graphs

  URL: https://github.com/fenderglass/Flye
  

  Command to load its environment: module load bioinfo/flye/2.9